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Deleting external/auxiliary files?For others who want to use this solution: Bibtex may not be too happy with this solution. Bibtex needs the aux file, but it also needs the bib file, which is (typically) not stored in the global aux folder. I fixed this by making bibtex search in a different folder (the same folder as the tex file -- that's where I store my bib file) for the bib file.